Contacts of the helix formed by residues 89 - 114 (chain I) in PDB entry 4NE1
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 89 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86I ALA 4.0 4.0 + - - +
87I ARG 4.2 1.7 - - - +
88I ARG* 1.3 77.9 + - - +
90I ASN* 1.3 65.0 + - - +
91I SER* 3.9 11.3 + - - -
92I LEU* 3.3 38.7 - - - +
93I LEU 3.5 4.3 + - - -
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Residues in contact with ASN 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87I ARG 4.0 14.6 + - - -
88I ARG 4.1 8.7 + - - +
89I SER* 1.3 72.6 - - - +
91I SER* 1.4 63.1 + - - +
92I LEU 3.2 0.2 - - - -
93I LEU* 3.5 12.7 + - + +
94I LYS* 3.2 27.9 + - - +
67J MET* 5.9 3.0 - - - +
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Residues in contact with SER 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89I SER* 3.9 11.5 + - - -
90I ASN* 1.4 75.3 - - - +
92I LEU* 1.3 59.3 + - - +
94I LYS* 3.7 17.0 + - - +
95I TYR* 3.0 27.2 + - - +
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Residues in contact with LEU 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I ALA* 3.7 27.6 - - + +
88I ARG* 6.4 0.2 - - + -
89I SER* 3.3 26.9 + - - +
91I SER* 1.3 81.2 + - - +
93I LEU* 1.3 58.8 + - - +
95I TYR* 3.2 11.9 + - + +
96I ILE* 2.8 53.9 + - + +
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Residues in contact with LEU 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I LYS* 3.2 38.1 - - + +
84I LEU* 5.5 1.3 - - + -
86I ALA 3.8 10.2 + - - +
87I ARG* 4.0 26.2 - - + +
89I SER 3.5 6.2 + - - +
90I ASN* 3.5 15.7 + - + +
92I LEU* 1.3 75.9 - - - +
94I LYS* 1.3 56.1 + - - +
96I ILE* 3.5 5.1 + - + -
97I THR* 3.1 42.8 + - + +
67J MET* 5.0 7.2 - - - -
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Residues in contact with LYS 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90I ASN 3.2 19.2 + - - +
91I SER* 3.7 18.3 + - - +
93I LEU* 1.3 73.2 - - - +
95I TYR* 1.3 62.2 + - - +
97I THR* 2.8 23.1 + - - +
98I ASP* 3.4 14.4 + - - +
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Residues in contact with TYR 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91I SER 3.0 17.5 + - - +
92I LEU* 3.3 16.8 - - + +
94I LYS* 1.3 73.9 - - - +
96I ILE* 1.3 76.4 + - + +
98I ASP* 3.4 10.8 + - - +
99I LYS* 3.2 53.4 + - + +
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Residues in contact with ILE 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I VAL* 5.5 3.4 - - + +
83I LYS* 3.6 38.6 - - + +
86I ALA* 4.1 20.2 - - + -
92I LEU* 2.8 44.0 + - + +
93I LEU* 3.7 9.0 - - + +
94I LYS 3.3 0.2 - - - -
95I TYR* 1.3 81.5 - - + +
97I THR* 1.3 54.7 + - - +
99I LYS* 3.1 7.1 + - + +
100I SER* 2.7 34.8 + - - -
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Residues in contact with THR 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I LYS* 3.8 24.7 - - + +
93I LEU* 3.1 22.5 + - + +
94I LYS* 2.8 23.1 + - - +
96I ILE* 1.3 74.8 - - - +
98I ASP* 1.3 64.0 + - - +
100I SER* 2.6 23.7 + - - -
101I GLU* 2.9 24.8 + - - +
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Residues in contact with ASP 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94I LYS* 3.4 12.3 + - - +
95I TYR* 3.4 12.4 + - - +
96I ILE 3.4 0.2 - - - -
97I THR* 1.3 77.6 + - - +
99I LYS* 1.3 68.2 + - + +
101I GLU* 3.2 16.9 + - - +
102I GLU* 3.2 24.1 + - - +
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Residues in contact with LYS 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95I TYR* 3.2 52.2 + - + +
96I ILE* 3.1 12.2 + - + +
98I ASP* 1.3 85.5 - - + +
100I SER* 1.3 64.2 + - - +
102I GLU* 3.7 31.7 + - - +
103I ILE* 3.3 25.0 + - - +
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Residues in contact with SER 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I THR* 5.0 11.8 - - - +
83I LYS* 3.3 36.9 + - - -
96I ILE* 2.7 18.5 + - - -
97I THR 2.6 18.9 + - - -
99I LYS* 1.3 73.1 - - - +
101I GLU* 1.3 60.9 + - - +
103I ILE* 3.2 28.2 - - - +
104I ALA* 3.2 9.4 + - - +
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Residues in contact with GLU 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I LYS* 5.8 0.7 + - - +
97I THR* 2.9 29.4 + - - +
98I ASP* 3.2 16.6 + - - +
100I SER* 1.3 78.9 + - - +
102I GLU* 1.3 65.0 + - - +
103I ILE 3.2 0.2 - - - -
104I ALA* 3.1 21.2 + - + +
105I GLN* 3.1 22.4 + - - +
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Residues in contact with GLU 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98I ASP 3.2 12.0 + - - +
99I LYS* 3.7 36.4 + - - +
101I GLU* 1.3 75.7 - - - +
103I ILE* 1.4 49.6 + - - +
105I GLN* 3.0 23.3 + - + +
106I ALA* 2.8 33.3 + - + +
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Residues in contact with ILE 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I THR* 4.7 22.9 - - + -
99I LYS 3.3 16.9 + - - +
100I SER* 3.2 19.3 - - - +
101I GLU 3.2 0.6 - - - -
102I GLU* 1.4 72.1 - - + +
104I ALA* 1.3 54.2 + - - +
106I ALA* 3.3 10.8 + - + +
107I ASN* 2.6 51.3 + - - +
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Residues in contact with ALA 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100I SER 3.2 9.4 + - - +
101I GLU* 3.1 19.7 + - + +
103I ILE* 1.3 75.2 - - - +
105I GLN* 1.3 57.2 + - + +
107I ASN* 3.1 32.5 - - - +
108I LEU* 3.3 16.0 + - - +
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Residues in contact with GLN 105 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101I GLU* 3.4 18.3 + - - +
102I GLU* 3.0 24.0 + - + +
104I ALA* 1.3 74.6 - - + +
106I ALA* 1.3 59.8 + - - +
107I ASN 3.2 1.3 - - - -
108I LEU* 3.4 33.5 + - + +
109I GLU* 3.6 14.1 + - - +
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Residues in contact with ALA 106 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102I GLU* 2.8 16.0 + - + +
103I ILE* 3.3 14.6 + - + +
105I GLN* 1.3 70.9 - - - +
107I ASN* 1.3 59.4 + - - +
109I GLU* 3.2 30.3 - - + +
110I ARG* 3.8 3.6 + - - +
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Residues in contact with ASN 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103I ILE* 2.6 40.6 + - - +
104I ALA* 3.1 27.0 - - - +
105I GLN 3.2 0.2 - - - -
106I ALA* 1.3 69.2 - - - +
108I LEU* 1.3 56.6 + - + -
109I GLU 3.2 2.0 - - - -
110I ARG* 3.0 28.2 + - - +
111I LYS* 3.7 5.4 + - - +
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Residues in contact with LEU 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104I ALA 3.3 13.2 + - - +
105I GLN* 3.4 25.7 + - + +
107I ASN* 1.3 75.5 - - + +
109I GLU* 1.3 63.1 + - - +
111I LYS* 3.2 21.5 + - + +
112I ALA* 3.3 12.1 + - - +
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Residues in contact with GLU 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105I GLN 3.6 12.8 - - - +
106I ALA* 3.2 23.6 - - + +
107I ASN 3.2 0.2 - - - -
108I LEU* 1.3 78.2 - - - +
110I ARG* 1.3 58.4 + - - +
112I ALA* 3.5 11.9 + - - +
113I GLN* 3.2 34.4 + - + +
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Residues in contact with ARG 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F T 5.2 6.9 + - - -
20F T 3.5 24.7 + - - -
106I ALA 3.8 3.1 + - - +
107I ASN* 3.0 16.6 + - - +
109I GLU* 1.3 77.4 - - - +
111I LYS* 1.3 73.6 + - - +
113I GLN* 3.3 34.8 + - + +
114I LYS* 3.5 36.5 + - + +
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Residues in contact with LYS 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107I ASN 3.7 4.5 + - - +
108I LEU* 3.2 14.4 + - + +
110I ARG* 1.3 88.6 - - + +
112I ALA* 1.3 58.9 + - - +
114I LYS 3.0 20.6 - - - +
115I LYS* 4.9 1.0 - - - -
116I LYS* 5.1 22.0 + - + +
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Residues in contact with ALA 112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108I LEU 3.3 11.3 + - - +
109I GLU* 3.7 15.3 - - - +
110I ARG 3.3 0.4 - - - -
111I LYS* 1.3 75.7 - - - +
113I GLN* 1.3 65.8 + - - +
114I LYS 4.1 3.3 - - - +
115I LYS* 4.4 6.8 + - - +
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Residues in contact with GLN 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109I GLU* 3.2 28.7 + - + +
110I ARG* 3.3 24.6 + - + +
112I ALA* 1.3 78.3 - - - +
114I LYS* 1.3 62.5 + - + +
115I LYS* 3.5 4.7 + - - +
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Residues in contact with LYS 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F T 3.7 31.3 + - - +
110I ARG* 3.5 31.7 + - + +
111I LYS* 3.0 22.1 - - - +
113I GLN* 1.3 78.1 - - + +
115I LYS* 1.3 67.2 + - - +
116I LYS* 4.0 18.8 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il